Twist of Fate
by wh1te rabb1t 01
Summary: An alternate universe story. Fate is a funny thing. Every second, thousands of choices pass, each one affecting the others. Life as we know it is an amazing series of lucky concidences. But what if luck failed that day on the freeway?
1. Prologue: Melissa Lyons

**

Twist of Fate

**

_"Fate, it seems, is not without a sense of irony."_****

* * *

**Prologue: [Melissa Lyons]**

"I don't want to hear it again," Melissa Lyons repeated as she sped down the freeway. "Give your sister her Barbie doll back."

"But Mom…"

"Samuel William Lyons, if you do not give your sister her doll back right now, the amount of trouble you will be in when I get home will be Biblical."

The voice on the other end of the line was sulky and beaten. "Fine…"

Melissa sighed and hung up. She turned the radio up.

_Video killed the radio star._

_ In my mind and in my car._

_ Can't rewind, we've gone too far._

Melissa absently hummed along with the music. She looked to the left and saw three police cruisers go shooting past her at well over ninety miles per hour.

_What the hell?_

Melissa switched the radio over to the news to try and gain some insight on what was happening. The radio announcer's voice filled the car.

"Police are reporting a fugitive from justice fleeing in a car on the highway just outside of the city. They have also reported another group of criminals are at large in the surrounding area. They are confident they will be able to capture – "

Melissa turned the volume down as her phone rang again. She answered it, rolling her eyes. As a result, she didn't see the biker approaching from the left.

"Yes?"

"Mommy," her youngest daughter whined, "he still has it!"

"Damn it!" Melissa cried as a crazy woman on a motorcycle cut in front of her. She jammed too hard on the brakes and skidded sideways, coming about so her car sat facing oncoming traffic. The last thing she ever saw was a Firebird car heading directly towards her, the driver, an African American woman, staring at her and slowly mouthing the word "shit."

Morpheus winced as the Agent lifted him up and held him.

"Only human," the Agent said in disdain. He threw him over the side. As Morpheus fell through the air, time seemed to slow. He clearly saw the empty ground underneath him and knew he would hit it. With equal clarity, he knew the car behind would swerve to avoid him but fail. He also knew the resulting pileup would prevent any traffic from reaching the truck.

Morpheus hit the ground, bones shattering. The oncoming car's brakes squealed as it swerved to try and miss the rebel captain. It failed, its rear wheels coming up and over Morpheus's head. 

_I failed… _he thought. _Forgive me, Neo. Forgive me, Zion._

There was a brief moment of fear and extreme pain, then everything faded into darkness.

The Agent walked towards the Keymaker, grabbing the Exile around the neck and lifting him high.

"We do only what we are meant to do," the Keymaker said slowly, sadly.

"And you are meant for only one thing," the Agent said coldly. "Deletion."

The Agent withdrew a syringe from his coat and pressed it into the Keymaker's neck, pushing the plunger down. 

_My purpose has not been fulfilled yet! _the Keymaker thought. _This must not happen!_

Despite his resistance, the program flowed into the Keymaker and quickly destroyed his code from the inside out. It was over quickly.

Neo flew the length of the freeway three times looking for survivors. Finally, he concluded there were none. He flew to the exit provided by a shocked Link and left the Matrix.

Trinity pulled the plug from his head and helped him sit up. He rested his head in his hands for a moment, overcome. Then he looked up at Trinity.

"What do I do now?"

His only answer was silence. The sound of the streaming code could be heard faintly in the distance.


	2. Oracle

**Chapter One: [Oracle]**

"Are you sure this is a good idea, Neo?" Link asked. "We should return to Zion."

"Link," Neo said, "the Keymaker was important. He's dead now. I don't know _what _I'm supposed to do. Without Morpheus's guidance…"

His voice failed him. He cleared his throat and went on.

"I don't know where we're going next. But I know there's one person who will. And that is the Oracle. So I'm going in to see her."

"Alright," Link said, beginning to type. "I'm loading you up."

Neo opened his eyes again inside the Matrix. He opened his cell phone.

"We're in."

He hung up and left the building, opening the door of the car parked outside. Trinity climbed into the driver's seat and turned the key, the engine roaring to life.

"Let's go," said Trinity, pressing down on the accelerator. The car leapt out into the street, and Trinity turned left and continued towards the Oracle's apartment.

They arrived at their destination five minutes later. Neo got out and walked inside, hitting the button to summon the elevator. Trinity joined him. They stood in silence as the elevator opened. They stepped in and it closed behind them, quickly rising towards the Oracle's floor.

The elevator beeped and they stepped out, walking towards the apartment. Neo reached for the knob and grabbed it, surprised when it didn't open before he touched it. He mentally shrugged and turned the knob.

The scene inside was a massacre. The Oracle's apartment was in shambles, furniture broken and thrown about everywhere. Neo heard voices from the kitchen and rushed forward, coming through the doorway.

He saw the Oracle seated at a table, waiting patiently. The two albino Twins from the Chateau stood over her, one holding a syringe in his left hand.

"The Merovingian warned you what would happen if you helped them," one of them said. They both turned as Neo entered the kitchen.

"You!" shouted the second one. The first moved forward, swinging a fist. Neo ducked under the attack and punched straight out, hitting the Twin in the stomach. He flew backwards and hit the wall, grunting. The second leapt into the air and kicked. Neo blocked the attack with a hand.

Trinity entered the kitchen, drawing a gun. She fired twice at One, who phased to avoid the bullets and jumped forward, returning to normal. He tackled her and they both went down.

Neo kicked high, Beta bending down and sideways to avoid the attack. Neo let his momentum carry, landing on the attacking foot as he brought the second one around. It smacked into the Twin with a thump and sent him flying.

Trinity slammed a fist into Alpha's cheek, the program tumbling off her. She rose to her feet in one graceful movement and rose into the air, arms outstretched, as the Twin rose. As he finished standing, her foot shot out and hit him in the neck, below the chin, and lifted up. His head snapped backwards and he fell to the floor.

Neo landed on both feet and ran after the Twin. Beta kicked off the wall and leapt at Neo, crashing into him at a high speed. Beta rose to his feet and flipped out his switchblade.

Trinity landed next to Alpha. The Exile suddenly shot his hand out, his switchblade going into Trinity's stomach. She cried in pain.

Neo ducked under a horizontal slash and jumped back as Beta brought the blade straight down. Neo grabbed the Exile's wrist and twisted, the blade dropping from his fingers. Holding his wrist, Neo punched Beta in the chest. Neo's fist passed the flesh and contacted Beta' code, leaving a huge hole in the Exile. The Twin fell to the ground, dead. Neo grabbed the Exile's dagger

Trinity gasped as her hands grabbed Alpha's wrist. She pushed the blade out and collapsed onto Alpha's chest. The Exile raised his blade high above, preparing to bring it down.

A knife came whistling through the air and struck Alpha in the hand. He hissed and turned to see Neo's fist descending downwards.

Neo laid Trinity out on the couch. She was shivering, so he covered her with a thin blanket. His hands moved to cover the area where she had been stabbed, and he closed his eyes, concentrating. He heard Trinity gasp.

He opened his eyes to see the wound gone, the flesh around the area pink and tender. He smiled as the Oracle came in.

"Thank you," she said. "I must confess, that didn't go exactly as I had thought it would. I fully expected you to reach the Source, until that Sam refused to give his sister the doll. Fate is a funny thing."

"Indeed it is," said Neo. "Why where those men here?"

"They came to delete me."

"Why?"

"The Merovingian warned me that if I chose to help you it would cost me. Now since the real test of any choice is to make it again, knowing what it will cost, I guess I feel pretty good about this one."

"What happens now?"

"There are things that you need to know, Neo, things that you would have found out if you had reached the Source, which you never will know. After I say these things, you'll probably be too angry at me to speak, and you'll just leave. So I beg of you to remember what I said the day we met."

And he listened as she began to explain about the previous Ones.

"Why didn't you tell me before?" he asked.

"You weren't ready," she replied.

"Who decided I wasn't ready?"

She pointed to the sign that hung over her doorway, the one that read "know thyself" in Latin.

"I did," Neo said.

"Exactly."

"What can I do now?" Neo asked. "Can Zion still be saved?"

"There are so many choices between here and there," the Oracle said, her voice growing heavier. "So many possibilities. Yes, Zion can be saved, but it will cost much."

"What must I do to save my city?"

"You know, Neo. You know where you must go. Though how you get there is anyone's guess."

As the elevator doors closed behind them, Neo turned to face Trinity, removing his glasses.

"Trinity…" he began. "I need to say something."

She looked at him, an invitation to continue.

"When I first flew over that stretch of highway, looking for survivors, I couldn't see anyone, or anything, besides wreckage and devastation. I thought you were dead. When I came out of there, back to the ship, and found you alive…Words can't describe how I felt.

"Back there in the room, when the Twin stabbed you, I felt it again. Like I might lose you. And Trinity, I couldn't bear that. Everything I thought I thought I had known has just been ripped away from me, and I'm glad you're here with me. The past few hours, Trinity…they've made me realize…"

His voice fell lower, until he was whispering.

"Just how much I love you."

He brought his lips into contact with Trinity's beginning the kiss. The elevator door reached the ground floor and beeped loudly, startling them both. With a slight grin, Neo replaced his glasses and stepped out.


	3. HammerSickle

**Chapter Two: [Hammer/Sickle]**

Roland stared at the Matrix feed, his eyes burning, willing it to be a lie. They had swept the Matrix many times and had found the same results every time.

_Morpheus…dead. Niobe…dead. Ghost…dead._

"Call Sparks," he ordered. "Find the _Logos. _We'll need that ship. Maggie, how's Bane doing?"

"No change yet, sir."

His eyes were red.

"I told them this would happen." Sparks said softly. "I always told them. But they never listened to me."

"Sparks," AK said patiently. "I feel for you, but we're coming to get you. Where's your ship?"

Sparks glanced to the side. "We're in an out-of-the-way spot down main line 32C. And get here quick, Squiddes are swarming all over the place."

"Alright," AK said. "Sparks?"

"What?"

"I'm sorry."

"Yea?" Sparks asked. "You know what? So am I."

He terminated the connection.

"Sir, we're coming up on the _Logos._"

Roland rubbed his eyes, suppressing a yawn.

"Bring us in."

The _Hammer _set down next to the _Logos, _lowering the door. Roland walked out, AK and Maggie walking after him. They climbed into the _Logos._ Sparks still sat at the operator's chair, staring at the Matrix feed. AK and Roland headed for the cockpit. Maggie glanced over and saw that it was a replay of the highway disaster.

"Right here," Sparks said, his throat raw, pausing the playback. The picture showed a young women yelling into a cell phone, as Trinity approached form the left on a bike.

"If I had been a little faster," he said. "Pressed the call button a little sooner…They could still be alive."

"Sparks," Maggie said. "You can't blame yourself."

Sparks slammed his fist into the keyboard, continuing the play. The two of them watched in silence as the car lost control and slammed into Niobe's vehicle.

"It is my fault," he said. "Nothing can change the fact that I wasn't fast enough, that I wasn't _good _enough. Maybe someone else could have saved them…but I couldn't. And now…"

He broke off, waving his hand to indicate where the bodies lay covered in sheets.

"It's working fine," AK said. "We've come up with a plan."

"If the _Logos _goes first," Roland continued, "We can punch an EMP here, at their weakest point. If we're lucky, the _Hammer _can get through the army. Now I have to ask one of you to undertake this mission…"

"I'll do it," Sparks said. "I've got no reason not to."

Roland nodded. 

"I'm going with him," Maggie said. Everyone turned to look at her.

"You'll need someone to help you," she explained. "I can drive better, anyway."

"That was a long time ago-" Sparks began to say angrily.

"Dammit, Sparks, I'm not going to let you drive off and kill yourself so easily. You want to die, I'm dying with you. Anyway, what's the difference between dying here and dying in Zion? Either way, we're just as dead."

The intercom beeped.

"Sir? Bane's waking up."

"What's his status?"

Roland leaned against the bulkhead tiredly.

"He claims he doesn't remember anything."

"That's a load of bullshit."

"I know. Watch him, will you?"

"Yes, sir."

Maggie hit the power button, and the _Logos _ rose onto its generators. 

"Ready?" she asked, turning to Sparks. He nodded.

"Charge the EMP."

Sparks flipped open the EMP casing and put his hand on the switch. 

"Let's go."

Maggie pulled the _Logos _into the air and shot forward. They zoomed past the smaller, slower _Hammer _and towards the Sentinel army, the _Hammer _close on their tail.

"Get ready," Maggie said. Sparks nodded again. They came out of the small pipe into the main pipe of the sewer system. Sentinels immediately spotted them and swarmed towards them.

"Here they come," Maggie said. "Hold fast."

"Lead them away!" Sparks yelled. Maggie turned left and shot towards the edge of the formation, Sentinels trailing after her. 

"NOW!" she yelled. Sparks slammed the EMP. The blue light swept through the cavern, knocking Sentinel's to the ground. Maggie turned in time to see the _Hammer _shoot through the pipe and past the Sentinel army.

The _Logos _began to fall. 

"Get to the back," Maggie yelled. They ran for the rear of the ship, but it was too late. The ship slammed into the rock wall, crushing the cockpit and throwing them from their spots into the Core. Then the _Logos _began to roll down the side of the tunnel. When they finally came to a stop, Maggie opened her eyes and looked down. She was covered in blood.

"Sparks?"

"We made it!" Roland shouted. Everyone cheered. "Call Zion. We'll need gate three open."

AK nodded and turned to his task. He reached for the console, but the lights onboard flickered and died.

"That maneuvering must have blown a fuse," Roland said. "Mauser, go check it."

"Yes, sir," he said, rising from his seat and heading downstairs.

"Here," he called, weakly. Maggie crawled over to find him.

"They made it," she said, taking his hand in hers. "They'll be coming for us soon."

Was that the clank of metal outside or just her imagination?

"I know."

"Sparks?"

"What?"

_That _was definitely something outside.

"It wasn't your fault."

"It was."

Sparks felt water touch his cheek and saw Maggie crying softly. He reached up and brushed a tear away from her eye.

"Hey," he said. "It's not _your _fault."

"I just wish I could have made you see reason before now."

There was a loud crash from outside, and the unmistakable buzzing sound of flying Sentinels.

"It's not too late," Sparks said. "Not yet."

Maggie leaned down to kiss him. There was a sudden increase in the buzzing from outside, a loud ripping sound and cold air flooded into the ship. Maggie broke her kiss and looked up, straight into the cold, red eyes of a Sentinel.

"Goodbye, Sparks."

"Goodbye."

Mauser slammed the fuse back into its housing and turned it sideways.

"Got it," he said, as strong hands encircled him from behind.

"Mister Aragon."

"What?" Mauser said.

"I remember you…a small little thing. Frightened, scared, like a _rodent._ You agreed to help us almost right away…but that Niobe tricked us, and you got away."

"Bane? What the hell are you talking about?"

"Oh, don't worry about it. It won't matter much longer anyway."

Mauser slammed his foot backwards into Bane's stomach. Bane gasped and let go. Mauser turned and slammed his foot into Bane's head, knocking the man over. Bane fell to his knees, grabbing a shard of glass.

"Bitch," Mauser said, cocking his foot back. Bane shot up, grabbing Mauser's side and slamming the glass into his neck. Mauser coughed once and fell, clawing at his throat. Bane placed his foot on Mauser's neck and pressed down until the rebel stopped struggling.

"Sir?"

"Yes, AK?"

"Zion confirms that it will open gate three for us when we are within range. They want us to punch the EMP as soon as we get there. Locke wants to talk with you."

Roland sat down in front of the view screen. "Yes, sir?"

"Captain Roland. Have you heard from Niobe?"

"Sir…"

"What is it?"

"Niobe was killed attempting to contact Morpheus."

Locke opened his mouth in shock, quickly covering his surprise and looking away. His fist clenched.

"I always knew he would be the death of her…When he gets back here…"

"Sir, Morpheus is dead too, as is Ghost, Sparks, and my medic, Maggie. We haven't heard from the _Neb, _but we assume the rest of them still live."

"Hurry to Zion," Locke said, ignoring Roland. "Or there won't be anything left to save."

Colt slammed the door to his room shut and sat on his bed, head in his hands. Headaches sucked, and this was one of the worst ones.

"Hello."

Colt looked up. Nothing. He shrugged.

A hand grabbed his shoulder. He whirled around and saw Bane. Bane slammed his hand into Colt's stomach and smiled. Colt was washed away by darkness.

"Sir, I can't find Colt or Mauser."

"We'll, have you checked the fuse area?"

"Not yet."

AK let himself down the hole, and spotted Mauser's corpse.

"Jesus H. Christ…" he whispered.

He turned around to spot Colt.

"Colt, thank God. I found Mauser!"

Colt grabbed him and pushed him back to the wall. Bane appeared from around the corner and walked forward, smiling evilly.

Roland saw AK and Colt enter the Core.

"You found him?"

AK nodded. Colt began to laugh. The door swung open and Bane entered, holding a plasma rifle.

"What the hell?" Roland asked. Bane fired.

"Commander Locke."

"Yes?"

"We have an entry at point one-seventeen."

"Tell Mifune."

"I already have."

"How long til the _Hammer _gets here?"

"Twenty minutes."

"This will be tight."

The _Hammer, _now controlled by the three real-world Smiths, continued its flight toward Zion. Bane looked over at Colt and smiled. The three erupted into eerie laughter.

"Mister Anderson…"


	4. Desert of the Real

**Chapter Three: [Desert of the Real]**

"Such destruction…" Neo whispered.

The _Nebuchadnezzar _had surfaced above the fields of growing humans. The three survivors sat silently sweeping the blackened sky and ground with their eyes. Trinity's hand found Neo's in the darkness and squeezed it tight.

"Why would they ever resort to something so drastic?" Neo asked out loud.

Trinity smiled faintly. "They were desperate. Desperate people do stupid things. In fifty years, they may think the same thing about our flight here and now. But we know it's something we must do."

Neo nodded. "I know."

"Let's go," Link said, reaching for their controls. The two tore their eyes away from the land beneath them and turned their attention to piloting the hovercraft.

"The city is coming up," Link announced a while later.

"Get ready," Neo said, slipping into his seat and buckling his harness around him. Trinity followed suit, taking the seat across from Neo. 

"Movement," Link warned.

A mile or so ahead, the ancient program stumbled out of its sleep-like state. Nothing had dared to come anywhere near its area of oversight for so long that the memories of it had been recycled.

It ordered the defenses to prepare. Far away, the massive weapons lifted themselves from their earthly constraints and readied their own weapons.

"What are they doing?" Trinity asked.

"Preparing to fire," Neo answered tonelessly. Millions of points of light appeared on the horizon, growing larger by the second.

"Here they come."

Link slammed the controls down, forcing the hovercraft into a dive. The _Neb _swerved under the first barrage of missiles and came back up on a straight heading as the weapons ahead loosed a second salvo. Link went high this time, dodging them again, but the third volley was already well on its way. Link cut the power and the _Neb _fell straight down, barely missing the bombs. Link hit the power again near the ground and the _Neb _shot forward towards the machine city.

The machines, however, had seen enough. They had analyzed the data and shot out a fourth barrage of bombs, this time over a wider spread of air. Link swerved around one but took a nick on the rear of the _Neb _from another. The _Neb _went into an out-of-control spin, tumbling wildly through the air.

It came to a slow stop just in time for the passengers to see the tow bomb heading straight for their cockpit.

Trinity groaned softly and tried to open her eyes the whole way, failing completely. She reached down and tried to untie her harness, finding the metal had completely fused together from the heat of the attack.

She fumbled under her seat for the emergency knife and cut the ropes. She fell, slamming into the floor of the cockpit. Glancing around as her vision cleared, she realized she had been hanging upside down.

_Probably why my head hurt…_

"Neo? Link?"

No answer. Trinity's breath came a little faster. She was trapped, alone, in the darkness of the machine's territory.

_Now's not the time, Trinity. Control yourself._

She gritted her teeth and began to search through the cockpit. She found Link lying under the pilot chair. She moved it aside and checked him for signs of life. Then she turned and looked for Neo. His chair was gone.

Neo awoke on the cold stone ground of the earth. The howling wind cut through his Zion uniform, chilling him to the bone. He pushed himself off the dirt and looked around for Trinity or Link.

No sign of either of them. He did, however, spot the wreck of the _Nebuchadnezzar. _He hurried towards it, ignoring the faint buzzing in the back of his mind.

A silent form entered the cockpit of the _Neb. _Trinity squinted, trying to make it out in the darkness.

"Neo?" she asked.

No verbal answer, but she saw the figure nod. It moved towards her, and she reached out, fumbling for a grip. Her hand finally came into contact with the other being's.

She instantly realized her mistake. The hand was cold and hard metal. She screamed as more metal hands grabbed her and carried her away.

Neo pushed open the side door, which fell off its hinges with a loud clang. He dropped inside the _Neb _and grabbed a flashlight and a small, one-shot plasma pistol from the emergency kit.

"Trinity!" he called, hoarsely, his throat dry. "Link!"

He heard a soft groan from the cockpit and hurried that way, shinging the flashlight.

The cockpit was a disaster. Small fires still burned in what was left of the original room. The chair where Neo had been sitting was no where to be seen. Trinity's chair was still intact, though, and Neo prayed he could find her alive.

Link lay on the floor of the cockpit, groaning. A large, red, scab covered the left side of his body.

"Something gored me in the crash," Link grunted. "The fire cauterized it."

Neo examined the wound.

"There's nothing you can do for me, friend…" Link breathed, coughing up a bit of blood.

"Link, have you seen Trinity?"

"She was in here when the Hunters came."

"Hunters?"

"New type of machine, one I'd only heard rumors about. They're supposed to be the ultimate human-killers."

"What happened to her?"

"They took her, Neo. Alive. Why, I don't know, but they took her. To 01."

"Thanks, Link."

The hologram unit nearby sputtered once and let out a shower of sparks. A blue light blinked weakly and then died.

"Sentinels," Link said. "Run, Neo, and I'll take out as many as I can."

Neo hit the earth ground with a thud. He rose to his feet and began to run towards a formation of caves, glancing behind him. The Sentinels were closing in on the downed hovercraft. One scanned it and flew past, towards the fleeing human in the distance.

_Shit, they're ignoring it._

One small cannon on the _Neb _opened up on the lead Sentinel. It exploded in a shower of flame. Neo silently cheered for Link.

The other Sentinels converged on the ship, firing their lasers into it. The cannon terminal was cut in half. It lay silent as the horde turned towards Neo.

A sudden roaring sound overtook Neo. He glanced backwards, and caught a glimpse of death before a wave of powerful wind knocked him to the ground. He sat up and wiped his lip clean of blood, looking back to where the _Neb _had been.

Nothing. It was gone, with most of the Sentinels. 

_Link! _Neo thought, almost despairing. _ They're all gone…I'm the last…_

Four of the Sentinels, however, had survived the operator's trap. They came towards Neo, buzzing and clicking.

_Now's not the time for mourning. That will come later._

He broke into another run for the nearby caves.

Neo reached the caves minutes before the Sentinels. He ducked inside one and grabbed a large rock, steadying himself. The first Sentinel showed itself at the opening, reaching a long tentacle into the cave. Neo fired his holdout weapon and the Sentinel spasmed and collapsed to the ground.

Neo lay back and watched as the Sentinel was dragged away. Two more faces appeared at the mouth of his cave, pushing their way in. He shined his flashlight directly on them and threw the first rock his hand found, braining one of the Sentinels on the head. It jerked around, slamming the other Sentinel away. Another sweeping tentacle hit a pillar of stone that Neo hid behind. He heard a rumble and knew the cave was about to collapse.

He ran outside, jumping over the three downed Sentinels. The fourth snapped around and midair and flew for him, slamming into his back and knocking him over. It circled around for another pass.

"No!" Neo yelled. He held out his hand and screamed, raw power surging through his body and into the oncoming Sentinel. It collapsed to the ground, all signs of life gone.

Neo climbed to his feet and took a step forward.

"Trinity…" he whispered.

He collapsed to his knees.

"Forgive…Me…"

He fell forward and hit the ground with a thud, eyes closed.


	5. Anvil

Disclaimer: I don't own the character of Jinx Travirez. It would be nice if I did, but I don't. She belongs to Insane Pineapple, from the excellent piece of writing known as "Constrained Tribulation." Please go read it. It's worth your time.

** Chapter Four: [Anvil]**

"Breach!"

Captain Mifune lifted the arms of his Armored Personal Unit towards the distant hole and opened fire. The nearby APUs copied his movement, and a massive cloud of bullets flew towards the oncoming Sentinels.

"Don't let them through!" Mifune yelled, shredding another Sentinel between his two guns. The hole above seemed to explode in a shower of metal as Sentinels came streaming out of the breach in every direction.

Zee ran along the top streets of the docks, glancing down to the battling forces. She grabbed an EMP grenade from her belt and crouched down, waiting.

With a loud crashing sound, the digger below began to lift itself onto its feet. She took careful aim and dropped her weapon.

The Sentinel army split into two arms, coming for the APU Corp in a deadly pincer movement. Mifune shifted fire, keeping one gun on each arm of the attack. Sentinels fell before the onslaught, but there were much more available.

There were always more.

The missile fell with deadly accuracy and hit the digger, exploding on contact. The EMP wave spread out over the machine, which went dark. The nearby Sentinels dropped to the ground. Zee saw small figures running away from the digger, and it suddenly exploded. Cheers sounded across the radio.

"Quiet!" Locke snapped. "It's not over yet. Second entry point detected."

Zee switched the radio off. From the hole above, three shapes emerged. They were similar to Sentinels, but were colored pitch-black, and they had two long metal arms underneath their "head."

They were Hunters. Zee turned and ran towards the center guns, the three Hunters sailing after her.

"Hunters in the docks!" Mifune cried. The APU beside him pointed both guns straight up and fired. A Hunter came on, weaving around the bullets and slammed straight into the APU. The massive machine teetered and fell into the city below.

The Hunter turned its attention to Mifune. He whirled one cannon towards the machine and opened fire, his bullets barley chipping the machine's titanium armor. Mifune brought his other cannon to bear and slowly backed towards the central gun tower.

"Sir," Locke's lieutenant cried, "The second digger has entered the docks! It's fallen near the entrance to the temple and is beginning to dig."

Locke nodded. "Send _her _to destroy it."

Zee crossed an invisible line, and the one of the gun towers swiveled towards her. It opened fire on the lead Hunter, pouring lead into the armor. The machine swerved out of the way and shot forward, grabbing Zee with one of its tentacles and pulling her back. She screamed as the thing raised itself up to kill her.

The gunner's tower tracked the target and fired again, the bullets slamming into the Hunter's weak spot: the external cooling unit. The Hunter wavered for a moment and then seemed to disintegrate. Fire replaced where it had been and spread out, driving the nearby Hunters away. Zee felt the heat wash over her and looked down.

She was on fire.

Two of the towers turned towards Mifune and opened fire on the Hunter tracking him. The beast lunged forward and slammed into Mifune's APU, knocking it over. Mifune rolled out of his seat as the Hunter struck down where he had just been. He grabbed hold of the APU's controls and the APU lifted its arm and slammed it through the Hunter's head. The Hunter's eyes flickered dimly and cut off, both machines collapsing on top of Mifune. Everything went black.

"Mifune!" Locke shouted into the radio. "Mifune!"

No answer. With a curse, Locke hurled the radio against the far wall.

Zee struggled against the fire, putting it out with much effort. On her hands and knees, she crawled towards the medical bay. Reaching it, she collapsed by the door with a gasp.

Snake ran across the bridge towards the center of the docks. Behind him the buzzing increased as the Hunter gained on him. It passed him quickly, and he felt a strong metal bar slam him onto the floor. He pushed himself back up as the Hunter turned around again.

The Hunter grabbed his shoulders with its strong arms and lifted him into the air. He kicked wildly as he was suspended over space. The Hunter opened its claws and let him drop. 

"Sir! The second digger has been destroyed!"

Locke activated the backup radio. "Travirez?"

"What?" came the soft voice across the radio.

"Wait there for the next one, and then take it out."

He quickly severed the connection before she could reply.

"Sir?"

"What?" he snapped, whirling around.

"The _Hammer _is two minutes away and requesting an open gate."

"Open gate two."

The massive doors slowly opened to let the hovercraft in. Bane glanced over at AK and laughed.

"Let's not keep them waiting."

The _Hammer _burst in through the Zion gate. The infantry and APU fighters paused to look on hopefully, and cheered as the blue light of an EMP spread out from the ship. 

Sentinels and Hunters collapsed to the ground. The remaining three APUs also jerked and fell, injuring their pilots. The _ Hammer _lost control and spun into the control tower, knocking the guns towers and power out. Darkness quickly fell.

"Where's your captain?" Locke demanded, wiping the smirk from AK's face. "I need to speak with him _now."_

Bane came up beside AK. "What's the problem, commander? We just saved your precious dock."

Locke glared, struggling for words to express his rage.

"Saved the dock? _Saved _the dock? You knocked out all the defenses and destroyed the control tower! You didn't save the dock, you just handed it over to the machines."

Bane was silent, nodding. "You're right. And if we've already given them the dock, I think the city of Zion would about even it out right?"

Locke looked confused. His face remained confused as Bane drew a knife and stabbed it deep into the commander's chest.

Bane laughed as Locke collapsed to the ground. The crowd around was stunned, frozen in a state of shock. Bane grabbed another knife from his belt and started towards Locke again, when a cold voice stopped him in his tracks.

"Freeze, Bane."

He turned around to see a woman standing next to Locke's fallen body. Jinx Travirez stood there coolly, head cocked slightly to the side.

Bane laughed. "Miss Travirez. So, they've let you roam free?"

AK and Colt moved up on either side of Bane, advancing towards Jinx. She turned a head over her shoulder and snapped at someone to get Locke to the medical wing.

"I don't know what you think you're doing," Jinx said, turning to face the Agents in disguise, "But I'm giving you one last chance to surrender peacefully."

Bane laughed. "There are three of us, pitiful human. Why would we surrender to _you?_"

Jinx didn't waste anymore time with words. She darted in, slamming a fist into Colt's throat and crushing his windpipe. AK ran towards Jinx, and she sidestepped and slammed the side of her palm into the base of his neck as he went past her. The man fell flat on the ground.

Bane was more cautious, beginning to circle around Jinx, who stood calmly in one place.

"You must excuse my overeager companions, Miss Travirez. This frail body takes some getting used to."

Jinx studied Bane. _Frail body…pathetic humans? What's going on?_

Bane suddenly exploded into motion, rushing straight at Jinx. She spun around and planted her feet, meeting Bane's charge. She caught him on her shoulder and threw him over her back. He hit the ground and rolled, coming to a stop a foot from the edge of the walkway.

He climbed to his feet and was hit in the stomach with a powerful kick. He fell, managing to catch himself on the ledge of the walkway. He glared up at Jinx.

"Kill this shell, Miss Travirez, bet it will not delay your doom."

Jinx felt realization dawning on her. "Smith?"

He laughed as her foot came down to crush his hands. He let go, falling and still laughing.

"Third entry point detected!"

The digger bored through the ceiling and fell to the ground below. A nearby lieutenant took charge, yelling for the infantry to fall back to the main city.

The Sentinels and Hunters poured through the hole, heading straight for the door. Two lead machines slammed themselves into the walkway, shattering it at the halfway point.

Jinx glanced around and saw a Hunter heading directly for her. She jumped and rolled, reaching up and grabbing a trailing tentacle as it shot past her. The Sentinel unwillingly carried her over the chasm and deposited her on the safer side of the walkway. She hit the ground running and raced into the elevator shaft to Zion, closing the door behind her with a slam.

Footsteps. He could hear footsteps in the distance, coming towards him. Locke peered into the gloom, searching for the sound's owner.

Jinx appeared before him, holding a single dim lamp. She placed it on the table beside his medical bed and glared down at him.

"Jinx…" he managed to choke out. "…Why?"

"Why did I save you?" Jinx asked. "I've asked myself the same question. For years you've tortured me, but I guess Zion is a little more important than personal revenge. And Zion needs you to survive this."

"How fares Zion?" Locke asked.

"Zion is lost," Jinx said. "And it no longer needs you, commander."

Groaning, Mifune returned to consciousness. He squirmed out from under the downed APU and glanced around him at his beloved city.

Zion was burning.


	6. Regeneration

** Chapter Five: [Regeneration]**

Neo awoke to the sound of thunder. He looked up at the sky to see the dark clouds boiling overhead. He shoved himself to his feet and looked around.

The last thing he could remember was the Sentinels. And the Hunter.

_Trinity._

He glanced around but didn't see the Sentinel's bodies anywhere near the caves. Come to think of it, the caves seemed somehow different, too.

Neo began to stagger back towards the wreck of the _Nebuchadnezzar, _climbing inside the hold and slowly making his way to the cockpit. Link's corpse was nowhere to be seen. He scanned the cockpit for anything that could help him, medical supplies or weapons so he could go and find Trinity-

_Stop it. The only chance you'll have is getting help from Zion. And the only chance that'll happen is if you either repair the ship – unlikely – or call for help._

Neo had a pounding headache in behind his forehead. He rubbed it irritably, trying to relieve the pain.

He leaned forward and hit the radio button. It exploded in a shower of sparks, sputtering briefly.

"Hello? Can anyone hear me? Hello?" There was a slight burst of static, and the radio went dead. Neo waited in silence for a long time.

After a long wait, the radio crackled to life. Over the air, Neo heard a voice he had never heard before, but one that was somehow familiar to him.

"Hello? Who's there?"

Neo eagerly hit the button. "This is the _Neb. _We're down and the crew is dead. I'm the only survivor. Who is this?"

"Hang on," the voice said. "We'll come get you."

The man signed off before Neo could respond. Neo settled down to wait with a nagging doubt at the back of his mind.

It was minutes until he realized what was wrong. The man had never asked where he was. He had just said, "We'll come get you." Who was "we"? And how did they know where Neo was? And why didn't they seem the least bit curious about what had happened to Neo?

Neo climbed out of the wreckage and looked across the land. He saw a group of three humans approaching him, walking strangely. As they came closer, he realized they were not humans at all.

"Oh my God…" Neo said.

They were half humans on one side, but the other side was completely metal. Their left eye was a blinking red socket and their left arm was a large circuit board. The metal stretched across their chests and down their left leg to the ground.

One spotted Neo and pointed. The three broke into a loping run, going faster than Neo had ever seen any human run. Neo scrambled down the _Neb _and ran for the caves.

Two more of the strange creatures appeared from nearby the caves. They had cut off his retreat. Neo wheeled around, dashing back for the _Neb. _He hit his foot on a lose rock and fell, hitting the ground with a thud.

A large group of the creatures appeared from the other side of the ship. Neo pushed himself to his feet and felt a strong hand grab him…a metal hand. The creature pulled him close and looked into his eyes.

"Let's take him back," he said. "They'll want to question him."

The others nodded.

They dragged him over the plains back towards a large vehicle, similar to a hovercraft. Instead of hover pads spread evenly over the body, it had two wings that the pads were spaced under.

They took him aboard and their leader led him back to a small room and sat him down in a chair.

"What's your name?" the creature asked.

"My name is…" Neo began. When he paused, the creature slammed his metal hand into Neo's cheek.

"Answer!"

"Phoenix!" Neo choked out. "My name is Phoenix!"

"Very well…Phoenix. What faction are you from? And how did you get by our scouts and arrive at the _Nebuchadnezzar _crash site?"

Neo blinked. "Faction?"

The creature tapped a foot impatiently against the floor.

"Don't toy with me, rebel. What faction?"

Neo felt the generators begin to come online. The ship lifted into the air and began to move with startling speed.

"Answer."

"I…I was going to 01."

The creature looked shocked. "01? Why?"

"To save Zion."

The creature looked at him blankly. He opened the door and left the room, swinging it shut behind him. It bounced on the frame and stayed open. What Neo heard made his blood run cold.

The creature returned and interrogated him further. Finally, he left, allowing Neo to get some sleep.

"Wake up, human!"

Neo was yanked from his chair and forced into the cockpit. The vehicle had stopped, hovering over a large body of dark water.

"Lake Michigan," the creature said. "We're told it's highly acidic no…too much so for human flesh. Tell us what you know or we'll find out if that's true."  
Neo had opened his mouth when another one of the half human's interrupted.

"Sir, we have rebels on the southern shore!"

"Bring us about," the leader snapped. "Destroy them!"

The aircraft turned and shot towards the shore, arriving there quickly. It lowered to near-ground level and back slowly creaked open. Three of the half humans jumped to the ground, holding plasma guns.

"Where are they?"

"No life forms detected…must have been a false reading."

"Let's get back aboard…AH!"

The ground beneath the three beasts gave away. Humans – true humans – appeared from all around, opening fire on the aircraft with strange weapons. Three of them concentrated fire on one wing, while a fourth ran up to the ship and jumped on board.

"Go!" the creature yelled. The cockpit emptied as the remaining fighters went to combat the human. The leader grabbed the controls and turned so the cockpit faced the humans, opening the trigger. Bullets cut through the air, taking down two of the fighters.

"Interceptors!"

The leader glanced up to see two similar craft approaching. Bullets cracked into the side of the wing. The ship began to spin out of control. Neo slammed his shoulder into the leader, driving him out and through the windshield.

The ship hit the ground with a crash and everything went black.

"Hello? Hello?"

Neo groaned and looked into a human face. 

"Are you Phoenix?"

"Yes," Neo said, climbing to his feet with the help of the human. They walked back outside, where six other humans stood.

"I found him, Kid," Neo's rescuer said, saluting a man older than the rest. The man looked at Neo strangely.

"Have we met?"

"I don't think so."

"I'm Raven," said a woman with black hair, reaching forward to shake his hand. "Welcome. What faction are you from?"

Neo shook his head.

"I don't know what's going on here. I don't know what those _things _were, or what this craft is. I don't know where I am. I don't know who you are. I have no idea what faction I'm from."

"Where are you?" Raven laughed. "Welcome to Babylon, the last human city."

"Babylon?"

"Yep."

"Have any of you ever heard of a city called Zion?"

There was scattered mutterings throughout the crowd. The older man stepped forward and stood in front of Neo, looking into his eyes.

"I was from Zion."

"Was?" Neo asked, dreading the answer.

"Phoenix, Zion was destroyed almost twenty years ago."


	7. Manifestations

**Chapter Six: [Manifestations]**

"No," Neo said. "You're lying. It can't be true."

"It's the sad truth," the man muttered. "I promise you."

"No…" Neo said, still not absorbing the fact. "It _can't _be. I went to save Zion!"

"Save Zion?" the man asked. "What are you talking about?"

"I…was on a mission," Neo said, coming back to where he was and who he was supposed to be…namely, not Neo.

"A secret mission to save Zion. We were heading straight for 01 with a new kind of computer virus. Before we got there, we were attacked by Sentinels…01 defenses shot us down."

The man chuckled softly at the confused looks on faces of his companions.

"Sentinels," he said. "Early, full-machine warriors. 01 was the first machine city."

He turned to Neo. "We better get you back to Babylon, Phoenix. It's not safe outside."

"Lead the way."

The small group gathered together and headed deeper into the ruins of Chicago. Their leader stopped in front of a large pile of rubble.

"We left the Scorpion here," he said, pushing away the rocks. The Scorpion was a large vehicle, similar to the tanks Neo had seen inside the Matrix. The exterior was large and bulky, makeshift armor bolted on all around. On the roof was mounted a large machine gun, and the back dropped open to admit the rebel troops. Raven climbed into the driver's seat, someone mounted the gunner's seat, and they started off.

The leader leaned back with a sigh of relief.

"We're never truly safe until we're, dead, of course," he smiled grimly, "but the Scorpion is one tough nut to crack." 

Neo nodded.

"So, let me introduce myself," the man continued. "I'm the leader of Babylon's defense corps…Everyone just calls me 'Kid.'"

Neo raised his eyebrows.

_It couldn't be…_

"The man in the gunner seat," Kid continued, "Is Glitch."

Glitch was a large, tough young man with black hair and cold eyes. He wore his tattered clothes with a sense of ease and gripped the large gun with steady hands. He nodded a greeting to "Phoenix," his eyes never leaving the sky around them.

"The man next to you is Prime."

Prime was older, but no less strong. He gripped Neo's hand firmly and looked into his eyes, smiling as if he liked what he saw there.

"You already met Raven…" Kid continued. The driver didn't acknowledge.

"The woman to your left is our medic, by the name of Maggie. We found her lying almost dead in the wreckage of a hovercraft not long after Zion was destroyed. If we had arrived a day later, she would have been dead from blood loss."

Maggie nodded coolly, not meeting Neo's eyes. Neo was thankful for that, fearing she might recognize him, even twenty years later. Her hair had grown gray and she seemed very tired.

"The younger woman on your other side is Nova."

Nova smiled.

"And these two twins are Hawk and Raptor."

Two heavily built men waved from the back of the truck. Hawk was slightly taller, and slightly thinner, busy cleaning his weapon, a long sniper rifle. Raptor was lost in deep thought, but he raised his eyebrows at Neo.

"Is this all of us left?" Neo asked, despairing. 

"No," Kid said. "There are a lot more back at Babylon. But our squad hasn't been back in a while. We were on our way back when we intercepted your transmission and came to rescue you. Then the Rapier hit us. If we hadn't been within flight distance of Babylon, we'd all be in a lot more pain right now."

Neo nodded. "What were those things that had me?"

Kid grinned slightly. "Wow, you really have been out of it. Those are the Seekers. They're half-human, half-machine; we don't know how. The machines must have captured someone from Zion. Their leader is a man named "Zero," and he's the best of all of them. He somehow senses humans. We think we know why, but we haven't been able to counter it."

"Why?"

"Well, we think it's because of special abilities he inherited from his father."

"Who was it?"

"A man named Neo."

Neo felt the world around him warp.

_What? No…It can't be…_

"You knew him, Phoenix?"

Neo swallowed. "Yes."

"We're here," Raven said, breaking the silence. Neo walked to the front and glanced out the forward windshield.

The massive wreckage of a huge tower was in front of them. Neo saw a gate slowly rising as the vehicle moved forward. Out of the corner of his eye, Neo saw gun emplacements tracking the vehicle in the surrounding buildings. An APU stalked forward on creaky legs, ready to sacrifice its life for a few extra seconds should machines attack.

The vehicle slowed to a halt inside Babylon.

"Welcome," Kid said, "To the last human city. Sorry about this."

"What?" Neo said. Kid pressed a small box to the back of Neo's neck, and the One fell forward to the deck.

"Take him to the interrogation rooms," Kid said. "Have _them_ meet him there."

Neo awoke on a small bed with a rather thin mattress. The metal bed bit into his back, and he sat up with a grown, fingering his head.

"Where am I?"

A door clanged and Neo looked up into a vaguely familiar face.

"Babylon," the man said. "You are Phoenix, correct?"

"Yes," Neo said.

"Good. We have some questions for you before you meet the Council."

"Questions?"

"Well, _ Phoenix, _you must admit that a man sleeping on the surface for twenty years is a bit unlikely. And this is not the first time the machines have tried to get an assassin inside Babylon. Once they succeeded, and…"

The man fell silent. He cleared his throat before going on.

"My wife died in that attack. So if you're serving the machines, you'll get no mercy from me."

"I'm sorry," Neo said. "But you can trust me. I've been fighting against the machines me entire life."

The man sighed and closed his eyes. "So had Ballard."

"Ballard betrayed us?"

"We don't know why. We think he went insane after being trapped in Babylon for so long. One day he grabbed hold of an APU and opened fire in the Council chambers. He killed three people, including Councillor Hammand, my wife, and another councillor."

Neo was silent. The interrogator was quiet too, reflecting. Eventually, he broke the silence and ordered Neo to come with him.

He led Neo down a long hallway into a room with a single wooden chair. Neo sat in the chair and the man attached two things to the side of Neo's head. He placed a small box on a table nearby.

"This is a lie detector," he explained. "It will tell us if you're answering truthfully or not. The interrogation will begin as soon as the head of security gets here."

Neo sat in silence for many minutes. He heard footsteps at the end of the hall and looked up, meeting the eyes of a man he assumed to be the head of security of Babylon. Neo felt a powerful jolt and saw a flicker of recognition in the man's eyes.

"This is Phoenix," Neo's interrogator said. The newcomer stopped him. 

"I know this man."

He came forward and crouched down in front of Neo.

"It's been a long time, Mister Anderson."

"Smith?" Neo gasped.

The interrogator looked from Smith to Neo.

"You know each other?"

"We know each other very well, Thompson. You were commissioned after the crash, so you never met the anomaly. This is the infamous _Neo._"

Smith's voice sneered slightly as he said Neo's name.

"What are you doing in a human city?" Neo finally asked.

"We're Babylon's security," Smith answered. "When the Matrix crashed, the humans offered to put us in the bodies of people who died during the attack on Zion. Our minds are capable of linking with their securities and protecting them to an extent no mere _human _could."

"The Matrix crashed?"

"The Architect was never human. He couldn't lie to you, Mister Anderson. But enough. I know someone who can explain what happened to Zion much better. After you meet the council, I will take you to see another old friend."


End file.
